X-132890476-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001394073.1(HS6ST2):​c.947+66332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 13694 hom., 14838 hem., cov: 18)
Failed GnomAD Quality Control

Consequence

HS6ST2
NM_001394073.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.359
Variant links:
Genes affected
HS6ST2 (HGNC:19133): (heparan sulfate 6-O-sulfotransferase 2) Heparan sulfate proteoglycans are ubiquitous components of the cell surface, extracellular matrix, and basement membranes, and interact with various ligands to influence cell growth, differentiation, adhesion, and migration. This gene encodes a member of the heparan sulfate (HS) sulfotransferase gene family, which catalyze the transfer of sulfate to HS. Different family members and isoforms are thought to synthesize heparan sulfates with tissue-specific structures and functions. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HS6ST2NM_001394073.1 linkc.947+66332G>A intron_variant Intron 2 of 4 ENST00000370833.7 NP_001381002.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HS6ST2ENST00000370833.7 linkc.947+66332G>A intron_variant Intron 2 of 4 5 NM_001394073.1 ENSP00000359870.3 Q96MM7-4

Frequencies

GnomAD3 genomes
AF:
0.567
AC:
59233
AN:
104427
Hom.:
13690
Cov.:
18
AF XY:
0.540
AC XY:
14785
AN XY:
27399
show subpopulations
Gnomad AFR
AF:
0.786
Gnomad AMI
AF:
0.459
Gnomad AMR
AF:
0.365
Gnomad ASJ
AF:
0.464
Gnomad EAS
AF:
0.467
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.513
Gnomad MID
AF:
0.589
Gnomad NFE
AF:
0.506
Gnomad OTH
AF:
0.540
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.567
AC:
59284
AN:
104480
Hom.:
13694
Cov.:
18
AF XY:
0.540
AC XY:
14838
AN XY:
27460
show subpopulations
Gnomad4 AFR
AF:
0.786
Gnomad4 AMR
AF:
0.365
Gnomad4 ASJ
AF:
0.464
Gnomad4 EAS
AF:
0.466
Gnomad4 SAS
AF:
0.489
Gnomad4 FIN
AF:
0.513
Gnomad4 NFE
AF:
0.506
Gnomad4 OTH
AF:
0.540
Alfa
AF:
0.543
Hom.:
3907
Bravo
AF:
0.568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.16
DANN
Benign
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7892161; hg19: chrX-132024504; API